CSI-TME: Spatial Isoform Analysis Dashboard

Cytokine & Secreted protein spatial Isoform distribution in the Tumor MicroEnvironment

Analysis Summary

24
Total Visium Samples
(ONT: 11, SR: 13)
32
Genes Analyzed
15
Genes Validated (scRNA)
194
Significant PSI Events

Validation Tier Summary

Validation Tiers:
TIER1_FULL Strong spatial + scRNA validation
TIER2_SPATIAL Reproducible spatial patterns only
TIER3_SCRNA scRNA validation but limited spatial
TIER4_PARTIAL Partial evidence in either modality

Key Findings

VCAN (Versican): Shows near-complete isoform switching (99% ΔPSI) between macrophages and tumor cells. The largest splicing effect in the dataset, validated both spatially (8/13 SR samples significant) and in scRNA-seq (p=1.4e-180).
APP (Amyloid Precursor Protein): Exon 7/8 inclusion varies dramatically between tumor states (MES: 82% vs NPC: 27%). Spatial HSIC-IR significant in 4/7 samples.
CLU (Clusterin): Most reproducible spatial isoform variation, significant in ALL 11 ONT samples (100%) and validated in scRNA-seq with 26 differential events.

Gene-Level Results

Gene ONT Sig ONT Best p SR Sig SR Best p Validation scRNA ΔPSI scRNA padj

Gene Details:

Sample-Level Results

Sample ID Platform Spots Genes Tested Genes Significant Best Gene Best p-value

Sample Details:

scRNA-seq Differential Splicing

32,304 cells from glioma scRNA-seq dataset. PSI values quantified by MARVEL.

Gene Event Type State 1 State 2 PSI 1 PSI 2 ΔPSI padj

Main Figures

SpaCET Deconvolution Plots

Cell type deconvolution showing VCAN isoform correlations with tumor vs macrophage content.

Spatial Isoform Maps

Spatial distribution of isoform ratios across tissue sections.

Download Data

Export analysis results and source data.

Source Files

Original data files in reports/ directory:

  • ont_splisosm_full_results.csv - ONT HSIC-IR results
  • pilot_splisosm_full_results.csv - SR HSIC-IR results
  • scrna_full_psi_differential.csv - All PSI comparisons
  • spacet_isoform_correlations.csv - Cell type correlations
  • final_validation_report.csv - Validation tier summary